Ligand Conformational Equilibrium in a Cytochrome P450 Complex

5 Ligand Conformational Equilibrium in a Cytochrome P450 Complex 

In this study we use REMD [67,75] to study the thermodynamic equilibrium between the conformations of the P450 BM-3/NPG complex in which the terminal carbon atoms of NPG is distant from the heme iron as in the low temperature X-ray crystal structure [147] (the distal state, see Fig. 5.2a) and conformations with the terminal carbon atoms of NPG proximal to the heme iron as in the conformation proposed by Jovanovic et al. [151] (the proximal state, see Fig. 5.2b). REMD is ideally suited for this problem not only because it improves conformational sampling but also because it yields the populations of conformational states over a range of temperatures. 

AGBNP [27] implicit solvent model to mimic the water environment. The replica exchange acceptance ratio was 25% on average. The total simulation time, including equilibration, was 3 ns for 24 replicas for a total of 72 ns. 

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